Hi Chris I would say there's something very wrong if you're seeing -6 sigma difference peaks at O atoms. I don't see how this can be explained by radiation damage. I for one have never seen that before in a structure where there weren't other obvious issues (or maybe I just haven't looked hard enough).
I would try refining it with a different program, e.g. Buster, or even a different version of Refmac (I use 5.6.x routinely, but I see there's a 5.7.x now - Garib will no doubt have an opinion on which is the best one to use). At least that will eliminate the software as the origin of the problem: if it doesn't go away then we'll have to think again. Cheers -- Ian On 4 April 2012 16:16, Chris Meier <crystallogra...@christophmeier.com> wrote: > Dear all, > I am refining the X-ray structure of a protein: > Data to ~2A were collected at a latest-generation synchrotron. > The 2fo-Fc maps are crisp, the model of the protein is complete and I am > reasonably happy with the stats (R below 20%, Rfree below 25% in Refmac 5.5). > However, I am seeing a lot of negative difference density, > especially around sulphur atoms (negative density around -9 sigma) > and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues with > negative density around -6 sigma). > Has anyone observed this before? > I have found CCP4bb postings discussing radiation damange of suplphur atoms > (e.g. http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html ). > Can this also happen with oxygen atoms? > What would be an appropriate way to deal with this issue during refinement? > Suggestions greatly appreciated. > Thanks, > Chris >
